Title :

ABSP: an automated R tool to efficiently analyze region-specific CpG methylation from bisulfite sequencing PCR

Author(s) :

Denoulet, Marie [Auteur]
Brulé, Mathilde [Auteur]
Anquez, François [Auteur]
Vincent, Audrey [Auteur]
Schnipper, Julie [Auteur]
Laboratoire de Physiologie Cellulaire et Moléculaire - UR UPJV 4667 [LPCM]
Adriaenssens, Eric [Auteur]
Toillon, Robert-Alain [Auteur]
Le Bourhis, Xuefen [Auteur]
Lagadec (Admin), Chann [Auteur]
Hétérogénéité, Plasticité et Résistance aux Thérapies des Cancers = Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 [CANTHER]

Journal title :

Bioinformatics

Publisher :

Oxford University Press (OUP)

Publication date :

2023-01-01

ISSN :

1367-4803

HAL domain(s) :

Sciences du Vivant [q-bio]

English abstract : [en]

Abstract Motivation Nowadays, epigenetic gene regulations are studied in each part of the biology, from embryonic development to diseases such as cancers and neurodegenerative disorders. Currently, to quantify and compare ...
Show more >Abstract Motivation Nowadays, epigenetic gene regulations are studied in each part of the biology, from embryonic development to diseases such as cancers and neurodegenerative disorders. Currently, to quantify and compare CpG methylation levels of a specific region of interest, the most accessible technique is the bisulfite sequencing PCR (BSP). However, no existing user-friendly tool is able to analyze data from all approaches of BSP. Therefore, the most convenient way to process results from the direct sequencing of PCR products (direct-BSP) is to manually analyze the chromatogram traces, which is a repetitive and prone to error task. Results Here, we implement a new R-based tool, called ABSP for analysis of bisulfite sequencing PCR, providing a complete analytic process of both direct-BSP and cloning-BSP data. It uses the raw sequencing trace files (.ab1) as input to compute and compare CpG methylation percentages. It is fully automated and includes a user-friendly interface as a built-in R shiny app, quality control steps and generates publication-ready graphics. Availability and implementation The ABSP tool and associated data are available on GitHub at https://github.com/ABSP-methylation-tool/ABSP. Supplementary information Supplementary data are available at Bioinformatics online.Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

Collections :

• Cancer Heterogeneity, Plasticity and Resistance to Therapies (CANTHER) - UMR 9020 - UMR 1277

Source :

Harvested from HAL